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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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PCoA with Euclidean distance fails with built-in "GlobalPatterns" dataset #645

Closed amckinlay closed 7 years ago

amckinlay commented 8 years ago 
> library("phyloseq")
> packageVersion("phyloseq")
[1] ‘1.16.2’
> data("GlobalPatterns")
> ordinate(GlobalPatterns, method = "MDS", distance = "euclidean")
Error in 1:(zero.eig[1] - 1) : NA/NaN argument
joey711 commented 7 years ago

Please update to the latest package... also, it might be that MDS on euclidean distance is supposed to fail when applied to an OTU table like GlobalPatterns...

Will close for now...

hk20013106 commented 6 years ago

Hi, I'm still receiving the same error message when running with v 1.25.3

packageVersion("phyloseq") [1] ‘1.25.3’ data("GlobalPatterns") ordinate(GlobalPatterns, method = "MDS", distance = "euclidean") Error in 1:(zero.eig[1] - 1) : NA/NaN argument

But when running the data(enterotype) (http://joey711.github.io/phyloseq/install.html ), it works perfectly. When following (http://joey711.github.io/phyloseq/install.html ) using my own data, I recieve the same err .

I don't know what is wrong with "GlobalPatterns" or my own data.

Any thought? Thanks!

rachaelantwis commented 4 years ago

Hi, did you manage to solve this? I'm having the same problem. Thanks.